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PLoS One. 2015 Jun 30;10(6):e0131106. doi: 10.1371/journal.pone.0131106. eCollection 2015.

Methodological Considerations in Estimation of Phenotype Heritability Using Genome-Wide SNP Data, Illustrated by an Analysis of the Heritability of Height in a Large Sample of African Ancestry Adults.

Author information

1
Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States of America.
2
Sylvester Comprehensive Cancer Center and Department of Epidemiology and Public Health, University of Miami Miller School of Medicine, Miami, FL, United States of America.
3
Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, United States of America.
4
The Cancer Institute of New Jersey, New Brunswick, NJ, United States of America.
5
Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States of America.
6
Division of Cancer Etiology, Department of Population Science, Beckman Research Institute, City of Hope, CA, United States of America.
7
International Epidemiology Institute, Rockville, MD, United States of America; Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University and the Vanderbilt-Ingram Cancer Center, Nashville, TN, United States of America.
8
Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University and the Vanderbilt-Ingram Cancer Center, Nashville, TN, United States of America.
9
The Translational Genomics Research Institute, Phoenix, AZ, United States of America.
10
Epidemiology Program, Cancer Research Center, University of Hawaii, Honolulu, HI, United States of America.
11
Cancer Prevention Institute of California, Fremont, CA, United States of America.
12
Epidemiology Research Program, American Cancer Society, Atlanta, GA, United States of America.
13
Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America.
14
Division of Epidemiology, Department of Environmental Medicine, New York University Langone Medical Center, New York, NY, United States of America.
15
Chronic Disease Research Centre and Faculty of Medical Sciences, University of the West Indies, Bridgetown, Barbados; Department of Preventive Medicine, Stony Brook University, Stony Brook, NY, United States of America.
16
Cancer Prevention Institute of California, Fremont, CA, United States of America; Division of Epidemiology, Department of Health Research & Policy, Stanford University School of Medicine and Stanford Cancer Institute, Stanford, CA, United States of America.
17
Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States of America.
18
Department of Preventive Medicine, Stony Brook University, Stony Brook, NY, United States of America.
19
Department of Epidemiology, Gillings School of Global Public Health, and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, United States of America.
20
Department of Urology, Northwestern University, Chicago, IL, United States of America.
21
Department of Biostatistics and Research Epidemiology, Henry Ford Hospital, Detroit, MI, United States of America.
22
Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States of America.
23
Department of Pathology, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States of America.
24
Department of Epidemiology, Harvard School of Public Health, Boston, MA, United States of America.
25
Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States of America.
26
Institute for Human Genetics, Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, United States of America.

Abstract

Height has an extremely polygenic pattern of inheritance. Genome-wide association studies (GWAS) have revealed hundreds of common variants that are associated with human height at genome-wide levels of significance. However, only a small fraction of phenotypic variation can be explained by the aggregate of these common variants. In a large study of African-American men and women (n = 14,419), we genotyped and analyzed 966,578 autosomal SNPs across the entire genome using a linear mixed model variance components approach implemented in the program GCTA (Yang et al Nat Genet 2010), and estimated an additive heritability of 44.7% (se: 3.7%) for this phenotype in a sample of evidently unrelated individuals. While this estimated value is similar to that given by Yang et al in their analyses, we remain concerned about two related issues: (1) whether in the complete absence of hidden relatedness, variance components methods have adequate power to estimate heritability when a very large number of SNPs are used in the analysis; and (2) whether estimation of heritability may be biased, in real studies, by low levels of residual hidden relatedness. We addressed the first question in a semi-analytic fashion by directly simulating the distribution of the score statistic for a test of zero heritability with and without low levels of relatedness. The second question was addressed by a very careful comparison of the behavior of estimated heritability for both observed (self-reported) height and simulated phenotypes compared to imputation R2 as a function of the number of SNPs used in the analysis. These simulations help to address the important question about whether today's GWAS SNPs will remain useful for imputing causal variants that are discovered using very large sample sizes in future studies of height, or whether the causal variants themselves will need to be genotyped de novo in order to build a prediction model that ultimately captures a large fraction of the variability of height, and by implication other complex phenotypes. Our overall conclusions are that when study sizes are quite large (5,000 or so) the additive heritability estimate for height is not apparently biased upwards using the linear mixed model; however there is evidence in our simulation that a very large number of causal variants (many thousands) each with very small effect on phenotypic variance will need to be discovered to fill the gap between the heritability explained by known versus unknown causal variants. We conclude that today's GWAS data will remain useful in the future for causal variant prediction, but that finding the causal variants that need to be predicted may be extremely laborious.

PMID:
26125186
PMCID:
PMC4488332
DOI:
10.1371/journal.pone.0131106
[Indexed for MEDLINE]
Free PMC Article

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